Should the rectangle vents on each side of the boat to the motor compartment be "scooping" air in? Mine appear to have the flaps facing as if to allow the air from in the compartment to flow out towards the back. It seems like they should be flipped around to scoop air in when your driving?

One set should be facing forward (the front set) and the others back.

On my 85 242, the port side are intakes, the starboard side are outflow.

The gen.premise is to create air circulation in order to constantly remove heat and fumes !

Actually you can put them anyway you want as they are under the boundary layer of airflow...